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Oliver GR, Blackburn PR, Ellingson MS, Conboy E, Pinto E Vairo F, Webley M, Thorland E, Ferber M, Van Hul E, van der Werf IM, Wuyts W, Babovic-Vuksanovic D, Klee EW. RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. Mol Genet Genomic Med 2019; 7:e00560. [PMID: 30632316 PMCID: PMC6418362 DOI: 10.1002/mgg3.560] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Background We describe a patient presenting with pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple osteochondromas. Methods The patient underwent extensive genetic testing and analysis in an attempt to diagnose the cause of his condition. Clinical testing included metaphase karyotyping, array comparative genomic hybridization, direct sequencing and multiplex ligation‐dependent probe amplification and trio‐based exome sequencing. Subsequently, research‐based whole transcriptome sequencing was conducted to determine whether it might shed light on the undiagnosed phenotype. Results Clinical exome sequencing of patient and parent samples revealed a maternally inherited splice‐site variant in the doublecortin (DCX) gene that was classified as likely pathogenic and diagnostic of the patient's neurological phenotype. Clinical array comparative genome hybridization analysis revealed a 16p13.3 deletion that could not be linked to the patient phenotype based on affected genes. Further clinical testing to determine the cause of the patient's multiple osteochondromas was unrevealing despite extensive profiling of the most likely causative genes, EXT1 and EXT2, including mutation screening by direct sequence analysis and multiplex ligation‐dependent probe amplification. Whole transcriptome sequencing identified a SAMD12‐EXT1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT1 function. Re‐review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD12 and EXT1 genes that corresponded precisely to the introns predicted to be affected by a fusion‐causing deletion. The existence of the mosaic deletion was subsequently confirmed clinically by an increased density copy number array and orthogonal methodologies Conclusions While mosaic mutations and deletions of EXT1 and EXT2 have been reported in the context of multiple osteochondromas, to our knowledge, this is the first time that transcriptomics technologies have been used to diagnose a patient via fusion transcript analysis in the congenital disease setting.
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Affiliation(s)
- Gavin R Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Filippo Pinto E Vairo
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Matthew Webley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew Ferber
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Els Van Hul
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ilse M van der Werf
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
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Wu Q, Xiao BO, Li LI, Feng LI. Atypical teratoid/rhabdoid tumor with hereditary multiple exostoses in an 18-year-old male: A case report. Oncol Lett 2015; 10:1561-1564. [PMID: 26622709 DOI: 10.3892/ol.2015.3389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/22/2015] [Indexed: 11/06/2022] Open
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is an aggressive embryonic brain tumor that is predominantly found in young children. The present study reports the unusual case of an adult male AT/RT patient with a history of another type of tumor, hereditary multiple exostoses (EXT or HME), who survived for 18 years. The patient's first and chief complaint was a 1-month history of progressive projectile vomiting. The patient was admitted twice for treatment, and on the second admission, a craniotomy was performed to remove a intracranial mass. However, no radiotherapy or chemotherapy treatment was administered. Pathology revealed monotonous medium- to large-sized neoplastic cells. The patient succumbed to a pulmonary infection and respiratory failure 14 days after the initial treatment. The prognosis for AT/RT is extremely poor; furthermore, the patient presented with another tumor. There may have been an association between the two tumors that worsened the clinical phenotype and prognosis of this patient. Additionally, symptomatic treatment for this condition is insufficient; early surgery and radiotherapy may be more useful for preventing the aggressive progression of these tumors.
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Affiliation(s)
- Qian Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - B O Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - L I Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - L I Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Tian C, Yan R, Wen S, Li X, Li T, Cai Z, Li X, Du H, Chen H. A splice mutation and mRNA decay of EXT2 provoke hereditary multiple exostoses. PLoS One 2014; 9:e94848. [PMID: 24728384 PMCID: PMC3984245 DOI: 10.1371/journal.pone.0094848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 03/20/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Hereditary multiple exostoses (HME) is an autosomal dominant disease. The classical paradigm of mutation screening seeks to relate alterations in the exostosin glycosyltransferase genes, EXT1 and EXT2, which are responsible for over 70% of HME cases. However, the pathological significance of the majority of these mutations is often unclear. METHODS In a Chinese family with HME, EXT1 and EXT2 genes were screened by direct sequencing. The consequence of a detected mutant was predicted by in silico analysis and confirmed by mRNA analysis. The EXT1 and EXT2 mRNA and protein levels and the HS patterns in the HME patients were compared with those in healthy controls. RESULTS A heterozygous transition (c.743+1G>A) in the EXT2 gene, which co-segregated with the HME phenotype in this family, was identified. The G residue at position +1 in intron 4 of EXT2 was predicted to be a 5' donor splice site. The mRNA analysis revealed an alternative transcript with a cryptic splice site 5 bp downstream of the wild-type site, which harbored a premature stop codon. However, the predicted truncated protein was not detected by western blot analysis. Decay of the mutant mRNA was shown by clone sequencing and quantification analysis. The corresponding downregulation of the EXT2 mRNA will contribute to the abnormal EXT1/EXT2 ratio and HS pattern that were detected in the patients with HME. CONCLUSION The heterozygous mutation c.743+1G>A in the EXT2 gene causes HME as a result of abnormal splicing, mRNA decay, and the resulting haploinsufficiency of EXT2.
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Affiliation(s)
- Chen Tian
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Rengna Yan
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shuzhen Wen
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Xueling Li
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Tianfeng Li
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Zhenming Cai
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Xinxiu Li
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
| | - Hong Du
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- * E-mail: (HD); (HC)
| | - Huimei Chen
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing, China
- * E-mail: (HD); (HC)
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